R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
#
# NOTE: This workflow is overkill for most R packages and
# check-standard.yaml is likely a better choice.
# usethis::use_github_action("check-standard") will install it.
on:
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master
  schedule:
    - cron: "10 0 * * *"

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}-${{ github.head_ref || github.sha }}-${{ github.base_ref || '' }}
  cancel-in-progress: true

name: rcc

jobs:
  rcc-smoke:
    runs-on: ubuntu-latest
    outputs:
      sha: ${{ steps.commit.outputs.sha }}

    name: "Smoke test: stock R"

    # Begin custom: services
    # End custom: services

    steps:
      - uses: actions/checkout@v3

      - uses: ./.github/workflows/rate-limit
        with:
          token: ${{ secrets.GITHUB_TOKEN }}

      - uses: ./.github/workflows/git-identity

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          install-r: false
          cache-version: rcc-smoke-2
          needs: check
          extra-packages: any::rcmdcheck any::roxygen2 r-lib/styler

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - uses: ./.github/workflows/update-snapshots
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

      - uses: ./.github/workflows/style
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

      - uses: ./.github/workflows/roxygenize
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

      - id: commit
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
        uses: ./.github/workflows/commit

      - uses: ./.github/workflows/check
        with:
          results: ${{ runner.os }}-smoke-test

  # Runs in a separate workflow, because it's using dev pkgdown
  # which might bring in other dev dependencies
  pkgdown:
    needs: rcc-smoke

    runs-on: ubuntu-latest

    name: "pkgdown"

    # Begin custom: services
    # End custom: services

    steps:
      - uses: actions/checkout@v3
        with:
          ref: ${{ needs.rcc-smoke.outputs.sha }}

      - uses: ./.github/workflows/rate-limit
        with:
          token: ${{ secrets.GITHUB_TOKEN }}

      - uses: ./.github/workflows/git-identity
        if: github.event_name == 'push'

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          install-r: false
          cache-version: pkgdown-1
          needs: website
          extra-packages: r-lib/pkgdown local::.

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - uses: ./.github/workflows/pkgdown-build
        if: github.event_name != 'push'

      - uses: ./.github/workflows/pkgdown-deploy
        if: github.event_name == 'push'

  # Windows checks can be run in parallel and independently
  # when they alone take as long as the smoke and full tests combined.
  # To achieve this, remove the "needs:" element below.
  rcc-windows:
    # Begin custom: early run
    needs: rcc-smoke
    # End custom: early run

    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.desc }}

    # Begin custom: services
    # End custom: services

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: windows-latest, r: 'release'}
          # Use 3.6 to trigger usage of RTools35

    steps:
      - uses: actions/checkout@v3
        with:
          ref: ${{ needs.rcc-smoke.outputs.sha }}

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          r-version: ${{ matrix.config.r }}
          cache-version: rcc-windows-1
          token: ${{ secrets.GITHUB_TOKEN }}
          needs: check

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - uses: ./.github/workflows/update-snapshots
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

      - uses: ./.github/workflows/check
        with:
          results: ${{ runner.os }}-r${{ matrix.config.r }}

  rcc-full:
    needs: rcc-smoke

    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.desc }}

    # Begin custom: services
    # End custom: services

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}

          - {os: ubuntu-20.04,   r: 'release'}

          # Use older ubuntu to maximise backward compatibility
          - {os: ubuntu-22.04,   r: 'devel',     http-user-agent: 'release'}
          - {os: ubuntu-22.04,   r: 'release',   covr: true,                  desc: 'with covr'}
          - {os: ubuntu-22.04,   r: 'oldrel-1'}

          # Begin custom: R 3.6
          - {os: ubuntu-22.04,   r: 'oldrel-2'}
          # End custom: R 3.6

          # Begin custom: R 3.5
          - {os: ubuntu-22.04,   r: 'oldrel-3'}
          # End custom: R 3.5

          # Begin custom: R 3.4
          # End custom: R 3.4

          # Begin custom: matrix elements
          - {os: ubuntu-20.04,   r: 'release',   test-src: 'test-mssql',      covr: false,   desc: 'SQL Server without covr' }
          - {os: ubuntu-22.04,   r: 'release',   test-src: 'test-postgres',   covr: true,   desc: 'Postgres with covr'   }
          - {os: ubuntu-22.04,   r: 'release',   test-src: 'test-maria',      covr: true,   desc: 'MariaDB with covr'   }
          - {os: ubuntu-22.04,   r: 'release',   test-src: 'test-mysql-maria', covr: true,   desc: 'MySQL with covr'   }
          - {os: ubuntu-22.04,   r: 'release',   test-src: 'test-duckdb',     covr: true,   desc: 'DuckDB with covr'     }
          - {os: ubuntu-22.04,   r: 'release',   test-src: 'test-sqlite',     covr: true,   desc: 'SQLite with covr'     }
          # End custom: matrix elements

    steps:
      - uses: actions/checkout@v3
        with:
          ref: ${{ needs.rcc-smoke.outputs.sha }}

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          r-version: ${{ matrix.config.r }}
          cache-version: rcc-full-1
          token: ${{ secrets.GITHUB_TOKEN }}
          needs: check

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - uses: ./.github/workflows/update-snapshots
        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

      - uses: ./.github/workflows/check
        with:
          results: ${{ runner.os }}-r${{ matrix.config.r }}

  suggests-matrix:
    runs-on: ubuntu-20.04
    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}

    name: Collect suggests deps

    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - uses: ./.github/workflows/rate-limit
        with:
          token: ${{ secrets.GITHUB_TOKEN }}

      - uses: r-lib/actions/setup-r@v2
        with:
          install-r: false
          use-public-rspm: true

      - id: set-matrix
        uses: ./.github/workflows/dep-matrix-suggests

  check-matrix:
    runs-on: ubuntu-22.04
    needs: suggests-matrix

    name: Check deps

    if: ${{ needs.matrix.outputs.matrix != '' }}

    steps:
      - name: Install json2yaml
        run: |
          sudo npm install -g json2yaml

      - name: Check matrix definition
        run: |
          matrix='${{ needs.matrix.outputs.matrix }}'
          echo $matrix
          echo $matrix | jq .
          echo $matrix | json2yaml

  rcc-suggests:
    needs:
      - suggests-matrix
      - rcc-smoke

    runs-on: ubuntu-22.04

    name: Without ${{ matrix.package }}

    if: ${{ needs.suggests-matrix.outputs.matrix != '' }}

    # Begin custom: services
    # End custom: services

    strategy:
      fail-fast: false
      matrix: ${{fromJson(needs.suggests-matrix.outputs.matrix)}}

    steps:
      - uses: actions/checkout@v3

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          install-r: false
          cache-version: rcc-dev-${{ matrix.package }}-1
          needs: check
          extra-packages: "any::rcmdcheck any::remotes ."
          token: ${{ secrets.GITHUB_TOKEN }}

      - name: Remove ${{ matrix.package }} and all strong dependencies
        run: |
          pkg <- "${{ matrix.package }}"
          pkgs <- tools::package_dependencies(pkg, reverse = TRUE)[[1]]
          installed <- rownames(utils::installed.packages())
          to_remove <- c(pkg, intersect(pkgs, installed))
          print(to_remove)
          remove.packages(to_remove)
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          if (!requireNamespace("sessioninfo", quietly = TRUE)) install.packages("sessioninfo")
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - name: Define _R_CHECK_FORCE_SUGGESTS_
        run: |
          cat('_R_CHECK_FORCE_SUGGESTS_=false\n', file = Sys.getenv("GITHUB_ENV"), append = TRUE)
        shell: Rscript {0}

      - name: Must allow NOTEs, even with _R_CHECK_FORCE_SUGGESTS_
        run: |
          if (Sys.getenv("RCMDCHECK_ERROR_ON") %in% c("", "note")) {
            cat('RCMDCHECK_ERROR_ON="warning"\n', file = Sys.getenv("GITHUB_ENV"), append = TRUE)
          }
        shell: Rscript {0}

      - name: Check env vars
        run: |
          print(Sys.getenv('_R_CHECK_FORCE_SUGGESTS_'))
          print(Sys.getenv('RCMDCHECK_ERROR_ON'))
        shell: Rscript {0}

      - uses: ./.github/workflows/check
        with:
          results: ${{ matrix.package }}

  # FIXME: integrate with dynamic matrix creation
  validate:
    needs:
      - rcc-smoke

    runs-on: ${{ matrix.config.os }}${{ matrix.config.os-version }}

    name: ${{ matrix.config.os }}${{ matrix.config.os-version }} (${{ matrix.config.r }}) ${{ matrix.config.desc }}

    # Begin custom: services
    # End custom: services

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-, os-version: 22.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      # prevent rgl issues because no X11 display is available
      RGL_USE_NULL: true
      # Begin custom: env vars
      # End custom: env vars

    steps:
      - uses: actions/checkout@v3

      - uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - uses: ./.github/workflows/install
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          install-r: false
          cache-version: rcc-smoke-1
          needs: check
          extra-packages: any::rcmdcheck any::roxygen2 r-lib/styler

      - uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - name: Instrument R code for validation
        run: |
          if [ $(git status --porcelain | wc -l) -gt 0 ]; then
            echo "Fatal: git working copy not clean"
          fi
          sed -i -r '/INSTRUMENT: validate/ s/^( +)# /\1/g' R/*
          if [ $(git status --porcelain | wc -l) -eq 0 ]; then
            echo "Fatal: substitution did not change anything"
          fi

      - name: Run tests
        run: |
          testthat::test_local(reporter = testthat::ProgressReporter$new(max_failures = Inf, update_interval = Inf))
        shell: Rscript {0}

      - name: Show test output
        if: always()
        run: |
          find check -name '*.Rout*' -exec head -n 1000000 '{}' \; || true
        shell: bash

      - name: Test coverage
        run: covr::codecov()
        shell: Rscript {0}